Transformer-based segmentation of adnexal lesions and ovarian implants in CT images

Two self-supervised pretrained transformer-based segmentation models (SMIT and Swin UNETR) fine-tuned on a dataset of ovarian cancer CT images provided reasonably accurate delineations of the tumors in an independent test dataset. Tumors in the adnexa were segmented more accurately by both transformers (SMIT and Swin UNETR) than the omental implants. AI-assisted labeling performed on 72 out of 245 omental implants resulted in smaller manual editing effort of 39.55 mm compared to full manual correction of partial labels of 106.49 mm and resulted in overall improved accuracy performance. Both SMIT and Swin UNETR did not generate any false detection of omental metastases in the urinary bladder and relatively few false detections in the small bowel, with 2.16 cc on average for SMIT and 7.37 cc for Swin UNETR respectively.

Self-supervised learning improves robustness of deep learning lung tumor segmentation to CT imaging differences

Self-supervised learning (SSL) is an approach to extract useful feature representations from unlabeled data, and enable fine-tuning on downstream tasks with limited labeled examples. Self-pretraining is a SSL approach that uses the curated task dataset for both pretraining the networks and fine-tuning them. Availability of large, diverse, and uncurated public medical image sets provides the opportunity to apply SSL in the "wild" and potentially extract features robust to imaging variations. However, the benefit of wild- vs self-pretraining has not been studied for medical image analysis. In this paper, we compare robustness of wild versus self-pretrained transformer (vision transformer [ViT] and hierarchical shifted window [Swin]) models to computed tomography (CT) imaging differences for non-small cell lung cancer (NSCLC) segmentation. Wild-pretrained Swin models outperformed self-pretrained Swin for the various imaging acquisitions. ViT resulted in similar accuracy for both wild- and self-pretrained models. Masked image prediction pretext task that forces networks to learn the local structure resulted in higher accuracy compared to contrastive task that models global image information. Wild-pretrained models resulted in higher feature reuse at the lower level layers and feature differentiation close to output layer after fine-tuning. Hence, we conclude: Wild-pretrained networks were more robust to analyzed CT imaging differences for lung tumor segmentation than self-pretrained methods. Swin architecture benefited from such pretraining more than ViT.

Deep learning classifier of locally advanced rectal cancer treatment response from endoscopy images

We developed a deep learning classifier of rectal cancer response (tumor vs. no-tumor) to total neoadjuvant treatment (TNT) from endoscopic images acquired before, during, and following TNT. We further evaluated the network's ability in a near out-of-distribution (OOD) problem to identify local regrowth (LR) from follow-up endoscopy images acquired several months to years after completing TNT. We addressed endoscopic image variability by using optimal mass transport-based image harmonization. We evaluated multiple training regularization schemes to study the ResNet-50 network's in-distribution and near-OOD generalization ability. Test time augmentation resulted in the most considerable accuracy improvement. Image harmonization resulted in slight accuracy improvement for the near-OOD cases. Our results suggest that off-the-shelf deep learning classifiers can detect rectal cancer from endoscopic images at various stages of therapy for surveillance.

Trustworthiness of Pretrained Transformers for Lung Cancer Segmentation

We assessed the trustworthiness of two self-supervision pretrained transformer models, Swin UNETR and SMIT, for fine-tuned lung (LC) tumor segmentation using 670 CT and MRI scans. We measured segmentation accuracy on two public 3D-CT datasets, robustness on CT scans of patients with COVID-19, CT scans of patients with ovarian cancer and T2-weighted MRI of men with prostate cancer, and zero-shot generalization of LC for T2-weighted MRIs. Both models demonstrated high accuracy on in-distribution data (Dice 0.80 for SMIT and 0.78 for Swin UNETR). SMIT showed similar near-out-of-distribution performance on CT scans (AUROC 89.85% vs. 89.19%) but significantly better far-out-of-distribution accuracy on CT (AUROC 97.2% vs. 87.1%) and MRI (92.15% vs. 73.8%). SMIT outperformed Swin UNETR in zero-shot segmentation on MRI (Dice 0.78 vs. 0.69). We expect these findings to guide the safe development and deployment of current and future pretrained models in routine clinical use.

Semantic Segmentation with Active Semi-Supervised Representation Learning

Obtaining human per-pixel labels for semantic segmentation is incredibly laborious, often making labeled dataset construction prohibitively expensive. Here, we endeavor to overcome this problem with a novel algorithm that combines semi-supervised and active learning, resulting in the ability to train an effective semantic segmentation algorithm with significantly lesser labeled data. To do this, we extend the prior state-of-the-art S4AL algorithm by replacing its mean teacher approach for semi-supervised learning with a self-training approach that improves learning with noisy labels. We further boost the neural network's ability to query useful data by adding a contrastive learning head, which leads to better understanding of the objects in the scene, and hence, better queries for active learning. We evaluate our method on CamVid and CityScapes datasets, the de-facto standards for active learning for semantic segmentation. We achieve more than 95% of the network's performance on CamVid and CityScapes datasets, utilizing only 12.1% and 15.1% of the labeled data, respectively. We also benchmark our method across existing stand-alone semi-supervised learning methods on the CityScapes dataset and achieve superior performance without any bells or whistles.

Semantic Segmentation with Active Semi-Supervised Learning

Using deep learning, we now have the ability to create exceptionally good semantic segmentation systems; however, collecting the prerequisite pixel-wise annotations for training images remains expensive and time-consuming. Therefore, it would be ideal to minimize the number of human annotations needed when creating a new dataset. Here, we address this problem by proposing a novel algorithm that combines active learning and semi-supervised learning. Active learning is an approach for identifying the best unlabeled samples to annotate. While there has been work on active learning for segmentation, most methods require annotating all pixel objects in each image, rather than only the most informative regions. We argue that this is inefficient. Instead, our active learning approach aims to minimize the number of annotations per-image. Our method is enriched with semi-supervised learning, where we use pseudo labels generated with a teacher-student framework to identify image regions that help disambiguate confused classes. We also integrate mechanisms that enable better performance on imbalanced label distributions, which have not been studied previously for active learning in semantic segmentation. In experiments on the CamVid and CityScapes datasets, our method obtains over 95% of the network's performance on the full-training set using less than 19% of the training data, whereas the previous state of the art required 40% of the training data.

AeroRIT: A New Scene for Hyperspectral Image Analysis

Hyperspectral imagery oriented research like image super-resolution and image fusion is often conducted on open source datasets captured via point and shoot camera setups (ICVL, CAVE) that have high signal to noise ratio. In contrast, spectral images captured from aircrafts have low spatial resolution and suffer from higher noise interference due to factors pertaining to atmospheric conditions. This leads to challenges in extracting contextual information from the captured data as convolutional neural networks are very noise-sensitive and slight atmospheric changes can often lead to a large distribution spread in spectral values overlooking the same object. To understand the challenges faced with aerial spectral data, we collect and label a flight line over the university campus, AeroRIT, and explore the task of semantic segmentation. To the best of our knowledge, this is the first comprehensive large-scale hyperspectral scene with nearly seven million semantic annotations for identifying cars, roads and buildings. We compare the performance of three popular architectures - SegNet, U-Net and Res-U-Net, for scene understanding and object identification. To date, aerial hyperspectral image analysis has been restricted to small datasets with limited train/test splits capabilities. We believe AeroRIT will help advance the research in the field with a more complex object distribution.

Tracking in Aerial Hyperspectral Videos using Deep Kernelized Correlation Filters

Hyperspectral imaging holds enormous potential to improve the state-of-the-art in aerial vehicle tracking with low spatial and temporal resolutions. Recently, adaptive multi-modal hyperspectral sensors have attracted growing interest due to their ability to record extended data quickly from aerial platforms. In this study, we apply popular concepts from traditional object tracking, namely (1) Kernelized Correlation Filters (KCF) and (2) Deep Convolutional Neural Network (CNN) features to aerial tracking in hyperspectral domain. We propose the Deep Hyperspectral Kernelized Correlation Filter based tracker (DeepHKCF) to efficiently track aerial vehicles using an adaptive multi-modal hyperspectral sensor. We address low temporal resolution by designing a single KCF-in-multiple Regions-of-Interest (ROIs) approach to cover a reasonably large area. To increase the speed of deep convolutional features extraction from multiple ROIs, we design an effective ROI mapping strategy. The proposed tracker also provides flexibility to couple with the more advanced correlation filter trackers. The DeepHKCF tracker performs exceptionally well with deep features set up in a synthetic hyperspectral video generated by the Digital Imaging and Remote Sensing Image Generation (DIRSIG) software. Additionally, we generate a large, synthetic, single-channel dataset using DIRSIG to perform vehicle classification in the Wide Area Motion Imagery (WAMI) platform. This way, the high-fidelity of the DIRSIG software is proved and a large scale aerial vehicle classification dataset is released to support studies on vehicle detection and tracking in the WAMI platform.

Aerial Spectral Super-Resolution using Conditional Adversarial Networks

Inferring spectral signatures from ground based natural images has acquired a lot of interest in applied deep learning. In contrast to the spectra of ground based images, aerial spectral images have low spatial resolution and suffer from higher noise interference. In this paper, we train a conditional adversarial network to learn an inverse mapping from a trichromatic space to 31 spectral bands within 400 to 700 nm. The network is trained on AeroCampus, a first of its kind aerial hyperspectral dataset. AeroCampus consists of high spatial resolution color images and low spatial resolution hyperspectral images (HSI). Color images synthesized from 31 spectral bands are used to train our network. With a baseline root mean square error of 2.48 on the synthesized RGB test data, we show that it is possible to generate spectral signatures in aerial imagery.

Aerial Vehicle Tracking by Adaptive Fusion of Hyperspectral Likelihood Maps

Hyperspectral cameras can provide unique spectral signatures for consistently distinguishing materials that can be used to solve surveillance tasks. In this paper, we propose a novel real-time hyperspectral likelihood maps-aided tracking method (HLT) inspired by an adaptive hyperspectral sensor. A moving object tracking system generally consists of registration, object detection, and tracking modules. We focus on the target detection part and remove the necessity to build any offline classifiers and tune a large amount of hyperparameters, instead learning a generative target model in an online manner for hyperspectral channels ranging from visible to infrared wavelengths. The key idea is that, our adaptive fusion method can combine likelihood maps from multiple bands of hyperspectral imagery into one single more distinctive representation increasing the margin between mean value of foreground and background pixels in the fused map. Experimental results show that the HLT not only outperforms all established fusion methods but is on par with the current state-of-the-art hyperspectral target tracking frameworks.